| Next changeset 1:27f670a42ba2 (2015-12-03) |
|
Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36 |
|
added:
README.rst segmentation-fold.xml test-data/test_01.dbn test-data/test_01.fa test-data/test_02.dbn test-data/test_02.fa test-data/test_03.dbn test-data/test_03.fa test-data/test_04.dbn test-data/test_04.fa test-data/test_05.dbn test-data/test_05.fa test-data/test_06.dbn test-data/test_06.fa test-data/test_07.dbn test-data/test_07.fa test-data/test_08.dbn test-data/test_08.fa test-data/test_09.dbn test-data/test_09.fa test-data/test_10.dbn test-data/test_10.fa test-data/test_11.dbn test-data/test_11.fa test-data/test_12.dbn test-data/test_12.fa test-data/test_13.dbn test-data/test_13.fa test-data/test_14.dbn test-data/test_14.fa test-data/test_15.dbn test-data/test_15.fa test-data/test_16.dbn test-data/test_16.fa test-data/test_17.dbn test-data/test_17.fa test-data/test_18.dbn test-data/test_18.fa test-data/test_19.dbn test-data/test_19.fa test-data/test_20.dbn test-data/test_20.fa test-data/test_21.dbn test-data/test_21.fa test-data/test_22.dbn test-data/test_22.fa test-data/test_23.dbn test-data/test_23.fa test-data/test_24.dbn test-data/test_24.fa test-data/test_25.dbn test-data/test_25.fa test-data/test_26.dbn test-data/test_26.fa test-data/test_27.dbn test-data/test_27.fa test-data/test_28.dbn test-data/test_28.fa tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 09e921a25c68 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,31 @@ +Segmentation-fold wrapper for Galaxy +==================================== + +https://github.com/yhoogstrate/segmentation-fold + +Segmentation-fold: An algorithm for predicting RNA 2D structures including K-turns + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate + +* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools + +The tool wrapper has been written by Youri Hoogstrate as MSc research +assignment at Technical University of Delft and University of Leiden. + +License +------- + +**segmentation-fold** and **wrapper**: + +GPL (>=3) + +References +---------- +Segmentaton-fold was formerly known as yh-kt-fold and the corresponding +thesis can be found at the following url: + +https://yh-kt-fold.googlecode.com/files/Report.pdf |
| b |
| diff -r 000000000000 -r 09e921a25c68 segmentation-fold.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentation-fold.xml Mon Aug 03 08:28:39 2015 -0400 |
| [ |
| b'@@ -0,0 +1,210 @@\n+<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0">\n+ <description>RNA-Folding including predefined segments including K-turns</description>\n+ \n+ <requirements>\n+ <requirement type="package" version="1.0.0">segmentation-fold</requirement>\n+ </requirements>\n+ \n+ <stdio></stdio>\n+ \n+ <version_command>segmentation-fold -V | head -n 2 | tail -n 1 | sed -e \'s/^[[:space:]]*//\' -e \'s/[[:space:]]*$//\'</version_command>\n+ \n+ <command><![CDATA[\n+ segmentation-fold\n+ \n+ #if $input.method == "fasta"\n+ -f $input.input_fasta\n+ #else\n+ -s $input.input_sequence\n+ #end if\n+ \n+ -p $predict_segments\n+ -h $min_hairpin_size\n+ \n+ #if $parameters.settings == "default"\n+ -x "${SEGMENTATION_FOLD_DEFAULT_XML}"\n+ #else\n+ -x $parameters.input_xml\n+ #end if\n+ \n+ -t \\${GALAXY_SLOTS:-2}\n+ > $output_dbn\n+ ]]></command>\n+ \n+ <inputs>\n+ \n+ <conditional name="input">\n+ <param name="method" type="select" label="Energy parameters">\n+ <option value="fasta" selected="true">As FASTA-file</option>\n+ <option value="text">As text</option>\n+ </param>\n+ <when value="fasta">\n+ <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" />\n+ </when>\n+ <when value="text"> \n+ <param name="input_sequence" type="text" label="RNA-sequece (-s)" />\n+ </when>\n+ </conditional>\n+ \n+ <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" />\n+ <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" />\n+ \n+ <conditional name="parameters">\n+ <param name="settings" type="select" label="Energy parameters">\n+ <option value="default" selected="true">Default</option>\n+ <option value="custom">Custom</option>\n+ </param>\n+ <when value="default" />\n+ <when value="custom"> \n+ <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom \'segments.xml\'-syntaxed file (-x)" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ \n+ <outputs>\n+ <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + \': \' + input.input_fasta.name if $input.method == \'fasta\' else $input.input_sequence.upper() }" />\n+ </outputs>\n+ \n+ <tests>\n+ <test>\n+ <param name="input_fasta" value="test_01.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_01.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_02.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_02.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_03.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_03.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_04.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_04.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_05.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_05.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_06.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_06.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_07.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_07.dbn" /'..b'fasta" value="test_13.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_13.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_14.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_14.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_15.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_15.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_16.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_16.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_17.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_17.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_18.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_18.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_19.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_19.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_20.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_20.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_21.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_21.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_22.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_22.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_23.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_23.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_24.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_24.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_25.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_25.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_26.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_26.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_27.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_27.dbn" />\n+ </test>\n+ <test>\n+ <param name="input_fasta" value="test_28.fa" ftype="fasta" />\n+ <output name="output_dbn" file="test_28.dbn" />\n+ </test>\n+ </tests>\n+ \n+ <help><![CDATA[\n+Segmentation-fold is a bioinformatics application that predicts RNA\n+2D-structure with an extended version of the Zuker algorithm. This\n+modification contains a new "structure element" named a segment and is\n+capable of folding a pre-defined substructure with multiple canonical\n+or non-canonical pairings.\n+\n+This allows folding of more complex structures like the K-turns, which\n+are also part of the implemented free energy tables. These thermodynamic\n+parameters (free Gibbs energy levels) have been estimated using a\n+computational approach and therefore lack accuracy.\n+ ]]></help>\n+ \n+ <citations>\n+ <citation type="bibtex">\n+ @mastersthesis{mastersthesis,\n+ author = {Youri Hoogstrate}, \n+ title = {An algorithm for predicting RNA 2D structures including K-turns},\n+ school = {University of Technology Delft, Leiden University},\n+ year = 2012,\n+ address = {},\n+ month = 11,\n+ note = {Research assignment for Master Computer-science},\n+ url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_01.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 34bp, dE: -32.2572 kcal/mole +CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG +((((((((((((.......)))...))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_01.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-7 +CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_02.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 34bp, dE: -34.4572 kcal/mole +CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG +((((((((((((..(...))))...))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_02.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-7 +CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_03.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 35bp, dE: -31.2572 kcal/mole +CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG +((((((((((((..(...)))))....)))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_03.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-7 +CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_04.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 34bp, dE: -30.4872 kcal/mole +CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG +((((((((((..((.....)))...))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_04.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-7 +CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_05.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 47bp, dE: -42.9072 kcal/mole +CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG +((((.(((((..(((((.((((....))))))))))))...)))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_05.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 16S rRNA containing Kt-11 +CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_06.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_06.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 47bp, dE: -41.3572 kcal/mole +GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC +((((.(((((..((((((.(((....))))))))))))...)))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_06.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_06.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 16S rRNA containing Kt-11 +GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_07.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 31bp, dE: -28.7072 kcal/mole +AACCGAAGCCCUCACGGGCAAUGUGGUGUCA +.((((.(((((....))))...))))).... |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_07.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-15 +AACCGAAGCCCUCACGGGCAAUGUGGUGUCA |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_08.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 37bp, dE: -33.7572 kcal/mole +UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG +((((((((((((((.(...))))...))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_08.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_08.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 16S rRNA containing Kt-23 +UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_09.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_09.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 37bp, dE: -30.8072 kcal/mole +UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG +((((((((((((((.(...))))...))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_09.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_09.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 16S rRNA containing Kt-23 +UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_10.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_10.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 109bp, dE: -82.9072 kcal/mole +CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG +((((((((((((.(((((((((((.((((.(((....))))).)).))))).(((.(((((.((((....))))..)))))...))))))))))))....))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_10.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_10.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-38 +CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_11.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_11.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 53bp, dE: -49.0072 kcal/mole +GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC +(((.((((((((((...((.((((((......))))))))))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_11.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_11.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-42 +GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_12.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_12.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 53bp, dE: -51.5072 kcal/mole +GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC +((.(((((((((((...((.((((((......))))))))))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_12.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_12.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-42 +GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_13.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_13.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 53bp, dE: -44.8072 kcal/mole +GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC +((.(((((((((((...((.((((((......))))))))))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_13.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_13.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-42 +GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_14.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 53bp, dE: -39.2072 kcal/mole +CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG +((.((..((..(((...((.((((((......)))))))))))..))..)))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_14.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_14.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-42 +CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_15.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_15.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 49bp, dE: -37.8572 kcal/mole +CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG +(.((((((((...(((((((((((....))))))))))))))))))).) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_15.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_15.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-46 +CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_16.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_16.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 50bp, dE: -44.4072 kcal/mole +UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA +(((((..((((...((((((((.((.....)))))))))))))).))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_16.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_16.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-46 +UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_17.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 49bp, dE: -38.8072 kcal/mole +UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA +(((((((.((...((((((((.((....)).)))))))))).))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_17.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_17.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-46 +UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_18.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 50bp, dE: -37.7072 kcal/mole +UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA +(((((.(.(((...(((((((((((....)))))))))))))).)))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_18.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_18.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-46 +UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_19.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_19.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 30bp, dE: -29.8572 kcal/mole +UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA +((((((((.((((...))))..)))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_19.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_19.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial 23S rRNA containing Kt-58 +UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_20.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_20.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 22bp, dE: -23.2072 kcal/mole +GCCAAUGAGGUUUAUCCGAGGC +(((...((((.....))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_20.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial U4 snRNA (small) +GCCAAUGAGGUUUAUCCGAGGC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_21.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 34bp, dE: -30.6072 kcal/mole +ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU +(((((.(((...(((((....))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_21.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_21.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Partial U4 snRNA (large) +ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_22.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_22.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 25bp, dE: -24.4072 kcal/mole +GCUCUGACCGAAAGGCGUGAUGAGC +(((((((((....))...))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_22.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_22.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>C/D-box snoRNA +GCUCUGACCGAAAGGCGUGAUGAGC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_23.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_23.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 85bp, dE: -70.7144 kcal/mole +GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC +((((((((...(((((((.((...(..(((((((((((((.....))))))))...)))))..)))))....))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_23.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_23.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>Artificial double C/D K-turn construct +GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_24.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_24.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 34bp, dE: -29.0072 kcal/mole +GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC +((((((...(((((((.....))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_24.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_24.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>L30e pre-mRNA +GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_25.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_25.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 26bp, dE: -24.7072 kcal/mole +GGUGGAGGGACUGGCCCGAUGAAACC +(((((((((.....)))...)))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_25.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_25.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>SAM riboswitch operon +GGUGGAGGGACUGGCCCGAUGAAACC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_26.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_26.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 55bp, dE: -43.9072 kcal/mole +GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC +((((((...(((((((....(((((((....))))...))).))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_26.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_26.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>T box +GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_27.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_27.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 36bp, dE: -26.2072 kcal/mole +AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU +(((...(((((((((((.....)))))))))))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_27.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_27.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>c-di-GMP-II aptamer +AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_28.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_28.dbn Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>Sequence length: 26bp, dE: -24.7072 kcal/mole +GGUGAAGGGACUGGCCCGACGAAACC +(((((((((.....)))...)))))) |
| b |
| diff -r 000000000000 -r 09e921a25c68 test-data/test_28.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_28.fa Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>G2nA SAM riboswitch +GGUGAAGGGACUGGCCCGACGAAACC |
| b |
| diff -r 000000000000 -r 09e921a25c68 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Aug 03 08:28:39 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="segmentation-fold" version="1.0.0"> + <repository changeset_revision="f4fce0d27352" name="package_segmentation_fold_1_0_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |